Manual

About

FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-04-05

All entries: 36946

Number of unique PDB entries: 7781

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FMODB ID: R8778

Calculation Name: 1NG2-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1NG2

Chain ID: A

ChEMBL ID:

UniProt ID: P14598

Base Structure: X-ray

Registration Date: 2023-09-24

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptHSide
Protonation MOE:Protonate 3D
Complement MOE:Structure Preparation
Water No
Procedure Auto-FMO protocol ver. 2.20220422
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 176
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1599729.312471
FMO2-HF: Nuclear repulsion 1529676.757742
FMO2-HF: Total energy -70052.554729
FMO2-MP2: Total energy -70258.152259


3D Structure
Snapshot
 
Ligand structure

ligand structure
Ligand Interaction
ligand interaction
Ligand binding energy
"
IFIE [kcal/mol] PIEDA [kcal/mol] Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level. ESElectro static interaction energy. EXExchange-repulsion energy. CT+mixCharge transfer and mixing terms energy. DI(MP2)Dispersion energy. q(I=>J)Charge transfer value from I to J fragments.
N/AN/AN/AN/AN/AN/A


Interactive mode: IFIE and PIEDA for fragment #1(A:157:ILE)


Summations of interaction energy for fragment #1(A:157:ILE)
IFIE [kcal/mol] PIEDA [kcal/mol] Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level. ESElectro static interaction energy. EXExchange-repulsion energy. CT+mixCharge transfer and mixing terms energy. DI(MP2)Dispersion energy. q(I=>J)Charge transfer value from I to J fragments.
-2.1130.5712.082-1.977-2.789-0.003
Interaction energy analysis for fragmet #1(A:157:ILE)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.005 / q_NPA : 0.004
Distance from base fragment(s) [Å]
Dist
Interaction energy by IFIE and PIEDA
[kcal/mol]
| Total | > | ES | > | EX | >
| CT+mix | > | DI(MP2) | >
Fragment charge [e]
FCHARGE q_Mulliken
q_NPA q(I=>J)
Residue
Res #    RES   
Sort
Graph Options
X Axis Label
Y Axis Max Y Axis Min
Display   
frag_NumFragment number. ChainChain species. Res #Residue number. RES3-letter code of amino acid residue, ligand and solvent molecule. FCHARGEFormal charge [e]. q_MullikenFragment charge evaluated by Mulliken charge [e]. q_NPAFragment charge evaluated by natural population analysis(NPA) charge [e]. DISTDistance from Ligand [Å]. TotalIFIE at MP2 level [kcal/mol]. ESElectro static interaction energy by PIEDA [kcal/mol]. EXExchange-repulsion energy by PIEDA [kcal/mol]. CT+mixCharge transfer and mixing terms energy by PIEDA [kcal/mol]. DI(MP2)Dispersion energy by PIEDA [kcal/mol]. q(I=>J)Charge transfer value from I to J fragmens [e].
3A159GLN00.0370.0092.560-1.0091.5682.083-1.971-2.689-0.003
4A160THR00.0010.0044.3060.2440.351-0.001-0.006-0.1000.000
5A161TYR00.0260.0146.7310.0400.0400.0000.0000.0000.000
6A162ARG10.9470.97310.2360.1480.1480.0000.0000.0000.000
7A163ALA00.0280.04213.599-0.016-0.0160.0000.0000.0000.000
8A164ILE0-0.047-0.04416.9900.0320.0320.0000.0000.0000.000
9A165ALA00.001-0.00419.7980.0170.0170.0000.0000.0000.000
10A166ASP-1-0.809-0.87421.408-0.114-0.1140.0000.0000.0000.000
11A167TYR0-0.099-0.06921.531-0.006-0.0060.0000.0000.0000.000
12A168GLU-1-0.893-0.94523.533-0.114-0.1140.0000.0000.0000.000
13A169LYS10.9020.95624.5020.1280.1280.0000.0000.0000.000
14A170THR0-0.058-0.03525.8930.0170.0170.0000.0000.0000.000
15A171SER00.0370.01626.7410.0160.0160.0000.0000.0000.000
16A172GLY0-0.052-0.03226.365-0.005-0.0050.0000.0000.0000.000
17A173SER0-0.047-0.02323.8640.0030.0030.0000.0000.0000.000
18A174GLU-1-0.748-0.84521.599-0.225-0.2250.0000.0000.0000.000
19A175MET0-0.048-0.01514.9940.0170.0170.0000.0000.0000.000
20A176ALA0-0.018-0.00720.758-0.005-0.0050.0000.0000.0000.000
21A177LEU0-0.048-0.03416.880-0.016-0.0160.0000.0000.0000.000
22A178SER00.0490.03719.9120.0180.0180.0000.0000.0000.000
23A179THR0-0.028-0.04919.609-0.013-0.0130.0000.0000.0000.000
24A180GLY0-0.100-0.05817.8680.0190.0190.0000.0000.0000.000
25A181ASP-1-0.822-0.90316.044-0.115-0.1150.0000.0000.0000.000
26A182VAL0-0.068-0.0459.966-0.024-0.0240.0000.0000.0000.000
27A183VAL00.017-0.00311.0580.0200.0200.0000.0000.0000.000
28A184GLU-1-0.859-0.9116.301-0.399-0.3990.0000.0000.0000.000
29A185VAL0-0.020-0.0277.3340.1220.1220.0000.0000.0000.000
30A186VAL0-0.044-0.0207.808-0.475-0.4750.0000.0000.0000.000
31A187GLU-1-0.949-0.97810.086-0.757-0.7570.0000.0000.0000.000
32A188LYS10.8280.9249.1111.0971.0970.0000.0000.0000.000
33A189SER00.0880.04313.5120.0230.0230.0000.0000.0000.000
34A190GLU-1-0.948-0.97617.251-0.327-0.3270.0000.0000.0000.000
35A191SER0-0.010-0.01519.8670.0370.0370.0000.0000.0000.000
36A192GLY0-0.029-0.01619.3500.0290.0290.0000.0000.0000.000
37A193TRP0-0.0280.00919.352-0.003-0.0030.0000.0000.0000.000
38A194TRP00.015-0.01211.952-0.089-0.0890.0000.0000.0000.000
39A195PHE00.0300.03613.6560.0510.0510.0000.0000.0000.000
40A196CYS0-0.030-0.02911.991-0.178-0.1780.0000.0000.0000.000
41A197GLN00.0040.0028.1640.0960.0960.0000.0000.0000.000
42A198MET00.0090.01611.349-0.046-0.0460.0000.0000.0000.000
43A199LYS10.7980.8805.6770.0980.0980.0000.0000.0000.000
44A200ALA00.002-0.00110.7580.0260.0260.0000.0000.0000.000
45A201LYS10.9770.99312.6650.0700.0700.0000.0000.0000.000
46A202ARG10.9650.9729.379-0.337-0.3370.0000.0000.0000.000
47A203GLY00.0320.00516.5400.0080.0080.0000.0000.0000.000
48A204TRP0-0.0080.00219.389-0.017-0.0170.0000.0000.0000.000
49A205ILE00.0260.01422.408-0.008-0.0080.0000.0000.0000.000
50A206PRO00.0150.00425.3180.0060.0060.0000.0000.0000.000
51A207ALA00.0930.04628.468-0.008-0.0080.0000.0000.0000.000
52A208SER0-0.015-0.02529.307-0.007-0.0070.0000.0000.0000.000
53A209PHE0-0.051-0.04330.076-0.007-0.0070.0000.0000.0000.000
54A210LEU0-0.0160.01425.620-0.005-0.0050.0000.0000.0000.000
55A211GLU-1-0.799-0.88029.9040.0100.0100.0000.0000.0000.000
56A212PRO00.0610.05229.414-0.003-0.0030.0000.0000.0000.000
57A213LEU00.023-0.00826.548-0.004-0.0040.0000.0000.0000.000
58A214ASP-1-0.864-0.92330.732-0.001-0.0010.0000.0000.0000.000
59A215SER0-0.038-0.04033.077-0.002-0.0020.0000.0000.0000.000
60A216PRO0-0.059-0.02734.2910.0020.0020.0000.0000.0000.000
61A217ASP-1-0.856-0.92135.8520.0230.0230.0000.0000.0000.000
62A218GLU-1-0.857-0.91230.7860.0520.0520.0000.0000.0000.000
63A219THR0-0.026-0.02030.541-0.004-0.0040.0000.0000.0000.000
64A220GLU-1-0.978-0.99927.3180.0760.0760.0000.0000.0000.000
65A221ASP-1-0.862-0.91631.8850.0660.0660.0000.0000.0000.000
66A222PRO0-0.045-0.01134.188-0.003-0.0030.0000.0000.0000.000
67A223GLU-1-0.876-0.95536.4250.0370.0370.0000.0000.0000.000
68A224PRO0-0.067-0.03440.0600.0040.0040.0000.0000.0000.000
69A225ASN0-0.001-0.00742.688-0.004-0.0040.0000.0000.0000.000
70A226TYR00.006-0.01444.4370.0010.0010.0000.0000.0000.000
71A227ALA00.0720.05247.570-0.001-0.0010.0000.0000.0000.000
72A228GLY0-0.0120.01445.6510.0000.0000.0000.0000.0000.000
73A229GLU-1-0.810-0.89040.2750.0780.0780.0000.0000.0000.000
74A230PRO00.0280.02544.3920.0000.0000.0000.0000.0000.000
75A231TYR0-0.016-0.03437.0030.0050.0050.0000.0000.0000.000
76A232VAL00.0090.00942.198-0.004-0.0040.0000.0000.0000.000
77A233ALA00.0150.02041.5960.0050.0050.0000.0000.0000.000
78A234ILE0-0.011-0.01436.007-0.001-0.0010.0000.0000.0000.000
79A235LYS10.9280.96636.213-0.086-0.0860.0000.0000.0000.000
80A236ALA0-0.0070.01340.402-0.002-0.0020.0000.0000.0000.000
81A237TYR0-0.104-0.08540.6750.0050.0050.0000.0000.0000.000
82A238THR00.0170.00643.126-0.001-0.0010.0000.0000.0000.000
83A239ALA0-0.025-0.00944.5840.0010.0010.0000.0000.0000.000
84A240VAL0-0.013-0.01442.919-0.002-0.0020.0000.0000.0000.000
85A241GLU-1-0.852-0.88742.8660.0360.0360.0000.0000.0000.000
86A242GLY0-0.002-0.01246.9320.0010.0010.0000.0000.0000.000
87A243ASP-1-0.851-0.90044.7960.0390.0390.0000.0000.0000.000
88A244GLU-1-0.768-0.85342.7800.0520.0520.0000.0000.0000.000
89A245VAL00.0020.00745.193-0.002-0.0020.0000.0000.0000.000
90A246SER0-0.012-0.00845.5100.0030.0030.0000.0000.0000.000
91A247LEU0-0.022-0.00244.146-0.001-0.0010.0000.0000.0000.000
92A248LEU00.003-0.00945.8670.0020.0020.0000.0000.0000.000
93A249GLU-1-0.938-0.98342.4300.0800.0800.0000.0000.0000.000
94A250GLY0-0.019-0.00945.042-0.002-0.0020.0000.0000.0000.000
95A251GLU-1-0.876-0.93346.9090.0490.0490.0000.0000.0000.000
96A252ALA0-0.009-0.01046.3910.0030.0030.0000.0000.0000.000
97A253VAL0-0.008-0.00444.421-0.003-0.0030.0000.0000.0000.000
98A254GLU-1-0.802-0.86746.0700.0500.0500.0000.0000.0000.000
99A255VAL0-0.041-0.02139.848-0.001-0.0010.0000.0000.0000.000
100A256ILE0-0.012-0.01843.3270.0000.0000.0000.0000.0000.000
101A257HIS00.0360.02639.207-0.003-0.0030.0000.0000.0000.000
102A258LYS10.8320.90036.002-0.080-0.0800.0000.0000.0000.000
103A259LEU0-0.0230.00735.4130.0030.0030.0000.0000.0000.000
104A260LEU00.0640.01529.6310.0070.0070.0000.0000.0000.000
105A261ASP-1-0.897-0.94230.9380.0630.0630.0000.0000.0000.000
106A262GLY0-0.032-0.02033.0360.0010.0010.0000.0000.0000.000
107A263TRP0-0.065-0.02733.8840.0000.0000.0000.0000.0000.000
108A264TRP00.0160.01334.029-0.002-0.0020.0000.0000.0000.000
109A265VAL0-0.0180.00439.360-0.002-0.0020.0000.0000.0000.000
110A266ILE0-0.007-0.00842.5760.0020.0020.0000.0000.0000.000
111A267ARG10.7730.83745.091-0.047-0.0470.0000.0000.0000.000
112A268LYS10.8660.92148.794-0.042-0.0420.0000.0000.0000.000
113A269ASP-1-0.845-0.90350.8070.0400.0400.0000.0000.0000.000
114A270ASP-1-0.903-0.94454.0870.0340.0340.0000.0000.0000.000
115A271VAL0-0.081-0.04752.089-0.002-0.0020.0000.0000.0000.000
116A272THR0-0.012-0.03047.7830.0010.0010.0000.0000.0000.000
117A273GLY00.000-0.00546.798-0.003-0.0030.0000.0000.0000.000
118A274TYR0-0.057-0.03340.8260.0020.0020.0000.0000.0000.000
119A275PHE00.0220.00540.360-0.001-0.0010.0000.0000.0000.000
120A276PRO0-0.0100.00536.2760.0020.0020.0000.0000.0000.000
121A277SER00.0330.01733.4390.0020.0020.0000.0000.0000.000
122A278MET0-0.028-0.02230.3870.0020.0020.0000.0000.0000.000
123A279TYR0-0.022-0.01434.0950.0060.0060.0000.0000.0000.000
124A280LEU00.0330.03637.054-0.005-0.0050.0000.0000.0000.000
125A281GLN0-0.012-0.02236.3690.0040.0040.0000.0000.0000.000
126A282LYS10.8690.93937.384-0.092-0.0920.0000.0000.0000.000
127A283SER00.007-0.01040.3520.0020.0020.0000.0000.0000.000
128A284GLY00.0180.00843.1160.0010.0010.0000.0000.0000.000
129A285GLN0-0.050-0.00938.3700.0070.0070.0000.0000.0000.000
130A286ASP-1-0.818-0.90737.0120.1100.1100.0000.0000.0000.000
131A287VAL00.1060.05237.2770.0060.0060.0000.0000.0000.000
132A288SER00.0490.04136.4510.0070.0070.0000.0000.0000.000
133A289GLN0-0.089-0.05932.3580.0170.0170.0000.0000.0000.000
134A290ALA00.008-0.00132.5820.0080.0080.0000.0000.0000.000
135A291GLN00.004-0.00833.2470.0080.0080.0000.0000.0000.000
136A292ARG10.8600.93630.138-0.137-0.1370.0000.0000.0000.000
137A293GLN0-0.072-0.03528.5680.0130.0130.0000.0000.0000.000
138A294ILE0-0.0330.00728.7450.0050.0050.0000.0000.0000.000
139A295LYS10.9360.95723.956-0.221-0.2210.0000.0000.0000.000
140A296ARG10.9070.96422.947-0.172-0.1720.0000.0000.0000.000
141A297GLY00.0160.01029.184-0.002-0.0020.0000.0000.0000.000
142A298ALA00.0140.00831.3980.0050.0050.0000.0000.0000.000
143A299PRO00.0050.00930.876-0.001-0.0010.0000.0000.0000.000
144A300PRO00.0600.04231.837-0.004-0.0040.0000.0000.0000.000
145A301ARG10.8800.94534.421-0.045-0.0450.0000.0000.0000.000
146A302ARG10.9150.94833.581-0.036-0.0360.0000.0000.0000.000
147A303SER0-0.078-0.07137.306-0.002-0.0020.0000.0000.0000.000
148A304SER0-0.043-0.02537.577-0.001-0.0010.0000.0000.0000.000
149A305ILE0-0.035-0.01135.070-0.001-0.0010.0000.0000.0000.000
150A306ARG10.9410.97039.068-0.021-0.0210.0000.0000.0000.000
151A307ASN0-0.011-0.02240.581-0.001-0.0010.0000.0000.0000.000
152A308ALA00.0030.01837.1660.0000.0000.0000.0000.0000.000
153A309HIS0-0.001-0.00835.903-0.004-0.0040.0000.0000.0000.000
154A310SER0-0.043-0.04335.1930.0000.0000.0000.0000.0000.000
155A311ILE0-0.006-0.00831.952-0.003-0.0030.0000.0000.0000.000
156A312HIS10.7540.88433.537-0.004-0.0040.0000.0000.0000.000
157A313GLN00.0420.01638.3770.0010.0010.0000.0000.0000.000
158A314ARG10.9090.96838.0670.0020.0020.0000.0000.0000.000
159A315SER00.0490.01840.7750.0000.0000.0000.0000.0000.000
160A316ARG10.9070.96935.950-0.040-0.0400.0000.0000.0000.000
161A317LYS10.8550.90640.108-0.016-0.0160.0000.0000.0000.000
162A318ARG10.8680.91337.028-0.044-0.0440.0000.0000.0000.000
163A319LEU00.0030.01942.858-0.002-0.0020.0000.0000.0000.000
164A320SER00.0480.02245.6610.0020.0020.0000.0000.0000.000
165A321GLN00.1250.04545.0160.0000.0000.0000.0000.0000.000
166A322ASP-1-0.769-0.83849.0310.0260.0260.0000.0000.0000.000
167A323ALA0-0.022-0.00949.5510.0000.0000.0000.0000.0000.000
168A324TYR00.001-0.02942.171-0.001-0.0010.0000.0000.0000.000
169A325ARG10.9050.94449.057-0.027-0.0270.0000.0000.0000.000
170A326ARG10.8150.88652.182-0.023-0.0230.0000.0000.0000.000
171A327ASN00.0260.01748.859-0.002-0.0020.0000.0000.0000.000
172A328SER00.0260.01250.1300.0010.0010.0000.0000.0000.000
173A329VAL0-0.020-0.01351.6450.0000.0000.0000.0000.0000.000
174A330ARG10.8440.92354.607-0.026-0.0260.0000.0000.0000.000
175A331PHE0-0.066-0.03251.368-0.001-0.0010.0000.0000.0000.000
176A332LEU00.0400.03951.2410.0030.0030.0000.0000.0000.000